diff --git a/.cargo/config b/config.toml
similarity index 100%
rename from .cargo/config
rename to config.toml
diff --git a/src/bam/record.rs b/src/bam/record.rs
index bae3742b6..c72627ec5 100644
--- a/src/bam/record.rs
+++ b/src/bam/record.rs
@@ -1088,30 +1088,36 @@ impl Record {
                 return SequenceReadPairOrientation::None;
             }
 
-            let (is_reverse, is_first_in_template, is_mate_reverse) = if self.pos() < self.mpos() {
-                // given record is the left one
+            let (pos_1, pos_2, fwd_1, fwd_2) = if self.is_first_in_template() {
                 (
-                    self.is_reverse(),
-                    self.is_first_in_template(),
-                    self.is_mate_reverse(),
+                    self.pos(),
+                    self.mpos(),
+                    !self.is_reverse(),
+                    !self.is_mate_reverse(),
                 )
             } else {
-                // given record is the right one
                 (
-                    self.is_mate_reverse(),
-                    self.is_last_in_template(),
-                    self.is_reverse(),
+                    self.mpos(),
+                    self.pos(),
+                    !self.is_mate_reverse(),
+                    !self.is_reverse(),
                 )
             };
-            match (is_reverse, is_first_in_template, is_mate_reverse) {
-                (false, false, false) => SequenceReadPairOrientation::F2F1,
-                (false, false, true) => SequenceReadPairOrientation::F2R1,
-                (false, true, false) => SequenceReadPairOrientation::F1F2,
-                (true, false, false) => SequenceReadPairOrientation::R2F1,
-                (false, true, true) => SequenceReadPairOrientation::F1R2,
-                (true, false, true) => SequenceReadPairOrientation::R2R1,
-                (true, true, false) => SequenceReadPairOrientation::R1F2,
-                (true, true, true) => SequenceReadPairOrientation::R1R2,
+
+            if pos_1 < pos_2 {
+                match (fwd_1, fwd_2) {
+                    (true, true) => SequenceReadPairOrientation::F1F2,
+                    (true, false) => SequenceReadPairOrientation::F1R2,
+                    (false, true) => SequenceReadPairOrientation::R1F2,
+                    (false, false) => SequenceReadPairOrientation::R1R2,
+                }
+            } else {
+                match (fwd_2, fwd_1) {
+                    (true, true) => SequenceReadPairOrientation::F2F1,
+                    (true, false) => SequenceReadPairOrientation::F2R1,
+                    (false, true) => SequenceReadPairOrientation::R2F1,
+                    (false, false) => SequenceReadPairOrientation::R2R1,
+                }
             }
         } else {
             SequenceReadPairOrientation::None
@@ -2844,6 +2850,32 @@ mod alignment_cigar_tests {
         }
     }
 
+    #[test]
+    fn test_read_orientation_f2r1() {
+        let mut bam = Reader::from_path(&"test/test_nonstandard_orientation.sam").unwrap();
+
+        for res in bam.records() {
+            let record = res.unwrap();
+            assert_eq!(
+                record.read_pair_orientation(),
+                SequenceReadPairOrientation::F2R1
+            );
+        }
+    }
+
+    #[test]
+    fn test_read_orientation_supplementary() {
+        let mut bam = Reader::from_path(&"test/test_orientation_supplementary.sam").unwrap();
+
+        for res in bam.records() {
+            let record = res.unwrap();
+            assert_eq!(
+                record.read_pair_orientation(),
+                SequenceReadPairOrientation::F2R1
+            );
+        }
+    }
+
     #[test]
     pub fn test_cigar_parsing_non_ascii_error() {
         let cigar_str = "43ጷ";
diff --git a/test/test_nonstandard_orientation.sam b/test/test_nonstandard_orientation.sam
new file mode 100644
index 000000000..d4d58d70b
--- /dev/null
+++ b/test/test_nonstandard_orientation.sam
@@ -0,0 +1,203 @@
+@HD	VN:1.6	SO:coordinate
+@SQ	SN:1	LN:248956422
+@SQ	SN:10	LN:133797422
+@SQ	SN:11	LN:135086622
+@SQ	SN:12	LN:133275309
+@SQ	SN:13	LN:114364328
+@SQ	SN:14	LN:107043718
+@SQ	SN:15	LN:101991189
+@SQ	SN:16	LN:90338345
+@SQ	SN:17	LN:83257441
+@SQ	SN:18	LN:80373285
+@SQ	SN:19	LN:58617616
+@SQ	SN:2	LN:242193529
+@SQ	SN:20	LN:64444167
+@SQ	SN:21	LN:46709983
+@SQ	SN:22	LN:50818468
+@SQ	SN:3	LN:198295559
+@SQ	SN:4	LN:190214555
+@SQ	SN:5	LN:181538259
+@SQ	SN:6	LN:170805979
+@SQ	SN:7	LN:159345973
+@SQ	SN:8	LN:145138636
+@SQ	SN:9	LN:138394717
+@SQ	SN:MT	LN:16569
+@SQ	SN:X	LN:156040895
+@SQ	SN:Y	LN:57227415
+@SQ	SN:KI270728.1	LN:1872759
+@SQ	SN:KI270727.1	LN:448248
+@SQ	SN:KI270442.1	LN:392061
+@SQ	SN:KI270729.1	LN:280839
+@SQ	SN:GL000225.1	LN:211173
+@SQ	SN:KI270743.1	LN:210658
+@SQ	SN:GL000008.2	LN:209709
+@SQ	SN:GL000009.2	LN:201709
+@SQ	SN:KI270747.1	LN:198735
+@SQ	SN:KI270722.1	LN:194050
+@SQ	SN:GL000194.1	LN:191469
+@SQ	SN:KI270742.1	LN:186739
+@SQ	SN:GL000205.2	LN:185591
+@SQ	SN:GL000195.1	LN:182896
+@SQ	SN:KI270736.1	LN:181920
+@SQ	SN:KI270733.1	LN:179772
+@SQ	SN:GL000224.1	LN:179693
+@SQ	SN:GL000219.1	LN:179198
+@SQ	SN:KI270719.1	LN:176845
+@SQ	SN:GL000216.2	LN:176608
+@SQ	SN:KI270712.1	LN:176043
+@SQ	SN:KI270706.1	LN:175055
+@SQ	SN:KI270725.1	LN:172810
+@SQ	SN:KI270744.1	LN:168472
+@SQ	SN:KI270734.1	LN:165050
+@SQ	SN:GL000213.1	LN:164239
+@SQ	SN:GL000220.1	LN:161802
+@SQ	SN:KI270715.1	LN:161471
+@SQ	SN:GL000218.1	LN:161147
+@SQ	SN:KI270749.1	LN:158759
+@SQ	SN:KI270741.1	LN:157432
+@SQ	SN:GL000221.1	LN:155397
+@SQ	SN:KI270716.1	LN:153799
+@SQ	SN:KI270731.1	LN:150754
+@SQ	SN:KI270751.1	LN:150742
+@SQ	SN:KI270750.1	LN:148850
+@SQ	SN:KI270519.1	LN:138126
+@SQ	SN:GL000214.1	LN:137718
+@SQ	SN:KI270708.1	LN:127682
+@SQ	SN:KI270730.1	LN:112551
+@SQ	SN:KI270438.1	LN:112505
+@SQ	SN:KI270737.1	LN:103838
+@SQ	SN:KI270721.1	LN:100316
+@SQ	SN:KI270738.1	LN:99375
+@SQ	SN:KI270748.1	LN:93321
+@SQ	SN:KI270435.1	LN:92983
+@SQ	SN:GL000208.1	LN:92689
+@SQ	SN:KI270538.1	LN:91309
+@SQ	SN:KI270756.1	LN:79590
+@SQ	SN:KI270739.1	LN:73985
+@SQ	SN:KI270757.1	LN:71251
+@SQ	SN:KI270709.1	LN:66860
+@SQ	SN:KI270746.1	LN:66486
+@SQ	SN:KI270753.1	LN:62944
+@SQ	SN:KI270589.1	LN:44474
+@SQ	SN:KI270726.1	LN:43739
+@SQ	SN:KI270735.1	LN:42811
+@SQ	SN:KI270711.1	LN:42210
+@SQ	SN:KI270745.1	LN:41891
+@SQ	SN:KI270714.1	LN:41717
+@SQ	SN:KI270732.1	LN:41543
+@SQ	SN:KI270713.1	LN:40745
+@SQ	SN:KI270754.1	LN:40191
+@SQ	SN:KI270710.1	LN:40176
+@SQ	SN:KI270717.1	LN:40062
+@SQ	SN:KI270724.1	LN:39555
+@SQ	SN:KI270720.1	LN:39050
+@SQ	SN:KI270723.1	LN:38115
+@SQ	SN:KI270718.1	LN:38054
+@SQ	SN:KI270317.1	LN:37690
+@SQ	SN:KI270740.1	LN:37240
+@SQ	SN:KI270755.1	LN:36723
+@SQ	SN:KI270707.1	LN:32032
+@SQ	SN:KI270579.1	LN:31033
+@SQ	SN:KI270752.1	LN:27745
+@SQ	SN:KI270512.1	LN:22689
+@SQ	SN:KI270322.1	LN:21476
+@SQ	SN:GL000226.1	LN:15008
+@SQ	SN:KI270311.1	LN:12399
+@SQ	SN:KI270366.1	LN:8320
+@SQ	SN:KI270511.1	LN:8127
+@SQ	SN:KI270448.1	LN:7992
+@SQ	SN:KI270521.1	LN:7642
+@SQ	SN:KI270581.1	LN:7046
+@SQ	SN:KI270582.1	LN:6504
+@SQ	SN:KI270515.1	LN:6361
+@SQ	SN:KI270588.1	LN:6158
+@SQ	SN:KI270591.1	LN:5796
+@SQ	SN:KI270522.1	LN:5674
+@SQ	SN:KI270507.1	LN:5353
+@SQ	SN:KI270590.1	LN:4685
+@SQ	SN:KI270584.1	LN:4513
+@SQ	SN:KI270320.1	LN:4416
+@SQ	SN:KI270382.1	LN:4215
+@SQ	SN:KI270468.1	LN:4055
+@SQ	SN:KI270467.1	LN:3920
+@SQ	SN:KI270362.1	LN:3530
+@SQ	SN:KI270517.1	LN:3253
+@SQ	SN:KI270593.1	LN:3041
+@SQ	SN:KI270528.1	LN:2983
+@SQ	SN:KI270587.1	LN:2969
+@SQ	SN:KI270364.1	LN:2855
+@SQ	SN:KI270371.1	LN:2805
+@SQ	SN:KI270333.1	LN:2699
+@SQ	SN:KI270374.1	LN:2656
+@SQ	SN:KI270411.1	LN:2646
+@SQ	SN:KI270414.1	LN:2489
+@SQ	SN:KI270510.1	LN:2415
+@SQ	SN:KI270390.1	LN:2387
+@SQ	SN:KI270375.1	LN:2378
+@SQ	SN:KI270420.1	LN:2321
+@SQ	SN:KI270509.1	LN:2318
+@SQ	SN:KI270315.1	LN:2276
+@SQ	SN:KI270302.1	LN:2274
+@SQ	SN:KI270518.1	LN:2186
+@SQ	SN:KI270530.1	LN:2168
+@SQ	SN:KI270304.1	LN:2165
+@SQ	SN:KI270418.1	LN:2145
+@SQ	SN:KI270424.1	LN:2140
+@SQ	SN:KI270417.1	LN:2043
+@SQ	SN:KI270508.1	LN:1951
+@SQ	SN:KI270303.1	LN:1942
+@SQ	SN:KI270381.1	LN:1930
+@SQ	SN:KI270529.1	LN:1899
+@SQ	SN:KI270425.1	LN:1884
+@SQ	SN:KI270396.1	LN:1880
+@SQ	SN:KI270363.1	LN:1803
+@SQ	SN:KI270386.1	LN:1788
+@SQ	SN:KI270465.1	LN:1774
+@SQ	SN:KI270383.1	LN:1750
+@SQ	SN:KI270384.1	LN:1658
+@SQ	SN:KI270330.1	LN:1652
+@SQ	SN:KI270372.1	LN:1650
+@SQ	SN:KI270548.1	LN:1599
+@SQ	SN:KI270580.1	LN:1553
+@SQ	SN:KI270387.1	LN:1537
+@SQ	SN:KI270391.1	LN:1484
+@SQ	SN:KI270305.1	LN:1472
+@SQ	SN:KI270373.1	LN:1451
+@SQ	SN:KI270422.1	LN:1445
+@SQ	SN:KI270316.1	LN:1444
+@SQ	SN:KI270340.1	LN:1428
+@SQ	SN:KI270338.1	LN:1428
+@SQ	SN:KI270583.1	LN:1400
+@SQ	SN:KI270334.1	LN:1368
+@SQ	SN:KI270429.1	LN:1361
+@SQ	SN:KI270393.1	LN:1308
+@SQ	SN:KI270516.1	LN:1300
+@SQ	SN:KI270389.1	LN:1298
+@SQ	SN:KI270466.1	LN:1233
+@SQ	SN:KI270388.1	LN:1216
+@SQ	SN:KI270544.1	LN:1202
+@SQ	SN:KI270310.1	LN:1201
+@SQ	SN:KI270412.1	LN:1179
+@SQ	SN:KI270395.1	LN:1143
+@SQ	SN:KI270376.1	LN:1136
+@SQ	SN:KI270337.1	LN:1121
+@SQ	SN:KI270335.1	LN:1048
+@SQ	SN:KI270378.1	LN:1048
+@SQ	SN:KI270379.1	LN:1045
+@SQ	SN:KI270329.1	LN:1040
+@SQ	SN:KI270419.1	LN:1029
+@SQ	SN:KI270336.1	LN:1026
+@SQ	SN:KI270312.1	LN:998
+@SQ	SN:KI270539.1	LN:993
+@SQ	SN:KI270385.1	LN:990
+@SQ	SN:KI270423.1	LN:981
+@SQ	SN:KI270392.1	LN:971
+@SQ	SN:KI270394.1	LN:970
+@RG	ID:chm	SM:chm	PL:ILLUMINA
+@PG	ID:bwa	PN:bwa	VN:0.7.17-r1188	CL:bwa mem -t 8 -R @RG\tID:chm\tSM:chm\tPL:ILLUMINA resources/genome.fasta results/merged/chm_R1.fastq.gz results/merged/chm_R2.fastq.gz
+@PG	ID:GATK ApplyBQSR	VN:4.1.4.1	CL:ApplyBQSR  --output results/recal/chm.sorted.bam --bqsr-recal-file /tmp/tmpuhppums6/recal_table.grp --input results/mapped/chm.sorted.bam --reference resources/genome.fasta  --preserve-qscores-less-than 6 --use-original-qualities false --quantize-quals 0 --round-down-quantized false --emit-original-quals false --global-qscore-prior -1.0 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false	PN:GATK ApplyBQSR
+@PG	ID:samtools	PN:samtools	PP:GATK ApplyBQSR	VN:1.20	CL:samtools view -H chm.bam
+@PG	ID:samtools.1	PN:samtools	PP:samtools	VN:1.20	CL:samtools view -b nonstandard_orientation.sam
+@PG	ID:samtools.2	PN:samtools	PP:samtools.1	VN:1.20	CL:samtools view -h test_nonstandard_orientation.bam
+HK35WCCXX160124:1:2117:25885:46859	163	1	231	46	113M38S	=	351	271	CAACCTCAGTTGACTTGGGGGACAAGGCAGCAGGAGCACCAGACCCCTGCACCACCTCCTTCTGGGTGGGAGATGAGGCAGCAGGAGCACCAGGGCCCTTCACGACCTCTTTCCAGGTGGGGGGGGAGGGAGCAGGGGCAGGAGAGCGCGT	=BB?BCBCABD@C@?D@AAABD@CB?B@C@ACABCAAC@BDAC@BCCCBBD@CD@CDCCCEC;BCCCBCCE?CCCBCDCECCECDDCCEA(.<BAADDBFCEA%C=DECEEFB</=C@#################################	XA:Z:1,+26345079,15S108M28S,3;1,+26344930,19S102M30S,2;	MC:Z:151M	MD:Z:90A0G11A9	RG:Z:chm	NM:i:3	AS:i:98	XS:i:93
+HK35WCCXX160124:1:2117:25885:46859	83	1	351	49	151M	=	231	-271	GGGATGAGGTAGCAGCGGCACCAGGGCCCTTCACAACCTCTTTTGAGGTGGGGGACGAGGCAGCAGGAGCACCAGACCCCTGCACCACCTCCTTCTGGGTGGGAGATGAGGCAGCAGGAGCACCAGGGCCCTTCACGACCTCTTTCCAGGT	##########################DA4ADCDCFDDCE;/BB.(10@DCB<CCC/1DCBBCBBDCCDBBCCB>:BBCBBDAABBABBACCADCBCBB?CBBA1BABAAA@@B@AABBAAACB?9BBABA@DDAC2BBBBCBCDBCCFA=?	XA:Z:1,-26345048,17S134M,8;	MC:Z:113M38S	MD:Z:1C7C5G0A28G5T4A46G32A14	RG:Z:chm	NM:i:9	AS:i:109	XS:i:94
diff --git a/test/test_orientation_supplementary.sam b/test/test_orientation_supplementary.sam
new file mode 100644
index 000000000..acf52140b
--- /dev/null
+++ b/test/test_orientation_supplementary.sam
@@ -0,0 +1,35 @@
+@HD	VN:1.3	SO:coordinate
+@SQ	SN:chr10	LN:135374737
+@SQ	SN:chr11	LN:134452384
+@SQ	SN:chr12	LN:132349534
+@SQ	SN:chr13	LN:114142980
+@SQ	SN:chr14	LN:106368585
+@SQ	SN:chr15	LN:100338915
+@SQ	SN:chr16	LN:88827254
+@SQ	SN:chr17	LN:78774742
+@SQ	SN:chr18	LN:76117153
+@SQ	SN:chr19	LN:63811651
+@SQ	SN:chr1	LN:247249719
+@SQ	SN:chr20	LN:62435964
+@SQ	SN:chr21	LN:46944323
+@SQ	SN:chr22	LN:49691432
+@SQ	SN:chr2	LN:242951149
+@SQ	SN:chr3	LN:199501827
+@SQ	SN:chr4	LN:191273063
+@SQ	SN:chr5	LN:180857866
+@SQ	SN:chr6	LN:170899992
+@SQ	SN:chr7	LN:158821424
+@SQ	SN:chr8	LN:146274826
+@SQ	SN:chr9	LN:140273252
+@SQ	SN:chrM	LN:16571
+@SQ	SN:chrX	LN:154913754
+@SQ	SN:chrY	LN:57772954
+@RG	ID:tumor	SM:tumor
+@PG	ID:bwa	PN:bwa	VN:0.7.16a-r1187-dirty	CL:resources/bwa mem -t 8 -Y -R @RG\tID:tumor\tSM:tumor index/hg18/genome reads/simulated.tumor.1.fastq reads/simulated.tumor.2.fastq
+@PG	ID:samtools	PN:samtools	PP:bwa	VN:1.20	CL:samtools sort -n -o tests/resources/testcases/test16/tumor.bam.namesorted.bam tests/resources/testcases/test16/tumor.bam
+@PG	ID:samtools.1	PN:samtools	PP:samtools	VN:1.20	CL:samtools fixmate tests/resources/testcases/test16/tumor.bam.namesorted.bam tests/resources/testcases/test16/tumor.bam.fixed.bam
+@PG	ID:samtools.2	PN:samtools	PP:samtools.1	VN:1.20	CL:samtools sort -o tests/resources/testcases/test16/tumor.bam tests/resources/testcases/test16/tumor.bam.fixed.bam
+@PG	ID:samtools.3	PN:samtools	PP:samtools.2	VN:1.20	CL:samtools view -H tumor.bam
+sim_Som2-5-1_chr1_1_1b5889	163	chr1	938	60	100M	=	1143	264	CACTATACCACTTGAATGCTCAGAAGAAAAAAAAAAGAATTCAGAATATGTGTATTAAAATGGGTACAATAATGAGTAAAAAACTTGAAAGAAGCTGGAG	GFGDECGFE?AA>FGADEEF)BDC>FDEC5EEBFEEB?D@BGDCAB:FBGGDE;DF-CBDDCD+>:ED@#?=?#>EADE,B#?A#FFC;CC@#:5DBA##	NM:i:1	MD:Z:69A30	AS:i:95	XS:i:23	ZT:Z:95,1,72,72,0,0,69,0,1,0,0,0,1379,0	RG:Z:tumor	MQ:i:60	MC:Z:59M41S
+sim_Som2-5-1_chr1_1_1b5889	83	chr1	1143	60	59M41S	=	938	-264	ATCTTTCCTTTATCAACTATTGGTGTTAACCTTTGATTATATTTTTGCATAAGCATACAAAATATTGATCTTTAATTATACTAAGGAATCAATAGCCAAA	F:##.##D#DFDA5D#*#:D?E7B?.>?GA>6?=CE:EEBEDAE=AF:5GF:G#ABGDGGAGEG=DAE?FF?GG7AGEG-BDEGDAGEDDEDF=>F5E*@	NM:i:2	MD:Z:2G13A42	AS:i:51	XS:i:20	SA:Z:chr1,73497948,-,58S42M,60,1;	ZT:Z:51,2,31,11,0,0,42,0,3,0,0,0,419,0	RG:Z:tumor	MQ:i:60	MC:Z:100M
+sim_Som2-5-1_chr1_1_1b5889	2131	chr1	1263	60	58S42M	=	938	-367	ATCTTTCCTTTATCAACTATTGGTGTTAACCTTTGATTATATTTTTGCATAAGCATACAAAATATTGATCTTTAATTATACTAAGGAATCAATAGCCAAA	F:##.##D#DFDA5D#*#:D?E7B?.>?GA>6?=CE:EEBEDAE=AF:5GF:G#ABGDGGAGEG=DAE?FF?GG7AGEG-BDEGDAGEDDEDF=>F5E*@	NM:i:1	MD:Z:40C1	MC:Z:100M	AS:i:40	XS:i:0	SA:Z:chr1,73497828,-,59M41S,60,2;	ZT:Z:40,1,40,40,0,0,40,0,0,0,0,0,400,0	RG:Z:tumor